Here's the situation. Impossible difficulty, Turn 87 or so. I'm seeing competent ships by my enemies, my fleet is overstretched, mostly veteran, my treasury is under constant threat of being empty and I can barely afford the maintenence. On the brighter side, despite my never researching, I've picked up quite a few techs from invasion, letting me catch up techwise.. halfway.

TAZ, the supreme dictator leader emperor of the Irakla, needs help. He leads the Alkari and gifted them repulsiveness, uncreativeness, Warlord, and transdimensionality. And threw them into a crowded advanced future in a large galaxy. Then, after refitting their two battleships, there was only war.
Colds have fallen.. but I have current troubles with two empires. Elerians and Klackons. There's an uneasy peace with the Meklars, but the psilons agreed without either side firing a shot.
HELP: Klackons take out my planet with this baby. Was NOT expecting anything remotely competent like this. How do you counter this - I've never dealt with missile ships on the other side.
This is the first Klackon BB built in a while. No doubt a dozen more are being built. Note: To be fair, a while is probably half a dozen turns.

My fleet is mostly made up of anti missile rocket DD's to protect my Mirv Nukers. That said:
I have the weakest tech. My fleet only outmasses any other empire by 2-1. My fusion drive is slow compared to their ion drive, often allowing enemies to hit me by surprise, but more importantly, making my missiles slower than theirs. my best beam is modded lasers; theirs is neutrons. I don't even have shields (yet).
2. I've been fighting fleets, starbases, battlestations, and missile bases that only have 1-6 missiles a ship, that are five shot, not two shot. But even two of these BB will definitely overwhelm me unless you can give me pointers. I saw this for the first time one turn ago. When it destroyed my planet, which coincidentally, was the only reason my fleet could reach Kholdan. But they have irridium fuel cells. I need some sort of long term strategy that can deal with being uncreative, and far behind the others tech wise (psilons have zort! graviton! everyone sides me and klackons have shields!) and tactics to take out these missile ships.

Interesting scenario. Are you not researching as an element of making the game harder for yourself? If not, you're bound to get something good eventually despite being uncreative, if you go through fields, chemistry, computers, etc. If so, are you allowing espionage? That could get a tech or two for you.

As far as tactics for what you have now, you might try a runner ship. Build one or two frigates with empty hulls, battle pods if possible, and augmented engines if possible. Depending on what tech you do have, you might be able to outrun missiles indefinitely with a ship like that. Then on your other ships, put 2 shot mirv nukes etc. In battle, unload nukes and retreat... leaving only the runner ships. Turn these around and run to the edges of the screen, until all your nukes hit. Hopefully you've inflicted losses on your enemy and your fleet survives entirely.
P.S. Scrap the anti missile rockets. They are not worth the space they take up. If you have battle scanners, you could use PD lasers, or maybe without battle scanners since you are warlord. But really outrunning missiles is probably the simplest low tech strategy. TransD should help with that. Runners are also effective against beams, since you have a fast ship with high beam defense and you are keeping yourself as far from the enemy ships as possible.
I'd say only use PD lasers if you need them to get out your second round of payload. Make sure you retreat the laser ships as well as the missiles after that.

Eventually your enemies (well, at least the psilons) will probably have effective beams. Hopefully you will have cobbled together enough tech to work something else out by then.

As far as tactics for what you have now, you might try a runner ship. Build one or two frigates with empty hulls, battle pods if possible, and augmented engines if possible. Depending on what tech you do have, you might be able to outrun missiles indefinitely with a ship like that. Then on your other ships, put 2 shot mirv nukes etc. In battle, unload nukes and retreat... leaving only the runner ships. Turn these around and run to the edges of the screen, until all your nukes hit. Hopefully you've inflicted losses on your enemy and your fleet survives entirely.

I'll try the missile runner ship tactic.
and let you know how it goes.

I just noticed, the Klakons have only Titanium Armor. This BB (or is it a Titan?) has only 160 hull points. Shoot with a tortchlight at it and it will fall apart. 10 Hv mass drivers or a hand full of Hv Fusion Beams, maybe even Lasers will shoot it down in one turn.